Antibiotics can significantly impact the microbiota and lead to infections including by Clostridium difficile (CDI). Investigators hypothesized that an altered metabolic environment may support CDI and therefore used 16S RNA gene sequencing and metabolomics to illuminate the changes in the gastrointestinal tract in a mouse model of CDI. Interestingly, resistance to CDI was conferred by distinct microbiome communities but, remarkably, the metabolic signatures were nearly identical across these distinct communities. Thus, 2 completely different microbial communities converged to a similar metabolic output and disease state. Bile acids were a key feature of this metabolic output. Taurocholate alone was shown to promote C. difficile germination and deoxycholate appeared to be inhibitory. These results build on a growing body of literature showing that, in addition to microbiome community structure being important to consider, the chemical output (metabolites) provide an important functional output for deciphering the relationship between the microbiome and health and disease.